Error in running the tutorial

[Tina9]

Hi,

I am running your tutorial (https://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html#6_Session_information), and met a problem when I run the code spectra(faahko). The error message is as follows: "Error: unable to find an inherited method for function ‘spectra’ for signature ‘object = "xcmsSet".

Besides, when I run faahko, the output is as follows: My sessionInfo() is as follows: """ R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.6.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Hong_Kong tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] MsExperiment_1.6.0 ProtGenerics_1.36.0 pheatmap_1.0.12
[4] pander_0.6.5 RColorBrewer_1.1-3 faahKO_1.44.0
[7] xcms_4.2.3 BiocParallel_1.38.0

loaded via a namespace (and not attached): [1] DBI_1.2.3 rlang_1.1.4
[3] magrittr_2.0.3 clue_0.3-65
[5] MassSpecWavelet_1.70.0 matrixStats_1.3.0
[7] compiler_4.4.1 vctrs_0.6.5
[9] reshape2_1.4.4 stringr_1.5.1
[11] pkgconfig_2.0.3 MetaboCoreUtils_1.12.0
[13] crayon_1.5.3 XVector_0.44.0
[15] utf8_1.2.4 UCSC.utils_1.0.0
[17] preprocessCore_1.66.0 purrr_1.0.2
[19] MultiAssayExperiment_1.30.3 zlibbioc_1.50.0
[21] GenomeInfoDb_1.40.1 jsonlite_1.8.8
[23] progress_1.2.3 DelayedArray_0.30.1
[25] parallel_4.4.1 prettyunits_1.2.0
[27] cluster_2.1.6 R6_2.5.1
[29] stringi_1.8.4 limma_3.60.4
[31] GenomicRanges_1.56.1 Rcpp_1.0.13
[33] SummarizedExperiment_1.34.0 iterators_1.0.14
[35] IRanges_2.38.1 Matrix_1.7-0
[37] igraph_2.0.3 tidyselect_1.2.1
[39] abind_1.4-5 doParallel_1.0.17
[41] codetools_0.2-20 affy_1.82.0
[43] lattice_0.22-6 tibble_3.2.1
[45] plyr_1.8.9 Biobase_2.64.0
[47] Spectra_1.14.1 pillar_1.9.0
[49] affyio_1.74.0 BiocManager_1.30.25
[51] MatrixGenerics_1.16.0 foreach_1.5.2
[53] stats4_4.4.1 MSnbase_2.30.1
[55] MALDIquant_1.22.3 ncdf4_1.23
[57] generics_0.1.3 S4Vectors_0.42.1
[59] hms_1.1.3 ggplot2_3.5.1
[61] munsell_0.5.1 scales_1.3.0
[63] glue_1.7.0 MsFeatures_1.12.0
[65] lazyeval_0.2.2 tools_4.4.1
[67] mzID_1.42.0 QFeatures_1.14.2
[69] vsn_3.72.0 mzR_2.38.0
[71] fs_1.6.4 XML_3.99-0.17
[73] grid_4.4.1 impute_1.78.0
[75] tidyr_1.3.1 MsCoreUtils_1.16.1
[77] colorspace_2.1-1 GenomeInfoDbData_1.2.12
[79] PSMatch_1.8.0 cli_3.6.3
[81] fansi_1.0.6 S4Arrays_1.4.1
[83] dplyr_1.1.4 AnnotationFilter_1.28.0
[85] pcaMethods_1.96.0 gtable_0.3.5
[87] digest_0.6.37 BiocGenerics_0.50.0
[89] SparseArray_1.4.8 lifecycle_1.0.4
[91] httr_1.4.7 statmod_1.5.0
[93] MASS_7.3-61
"""

Many thanks for your help.

[jorainer]

Sorry for my late reply. This is a bit surprising, because if you follow the steps in the xcms package you referenced above (which is this one, and refers to version 4.2.3 of xcms) the faahko variable should be a XcmsExperiment object, not a xcmsSet object. Can it be that the faahko variable you loaded/used is from an old version of the package?

[stanstrup]

This happens when you do not create the faahko object using readMsExperiment as shown in the tutorial. Then the faahko object from the faahKO package is used instead. This object is an xcmsSet object. So you have to create the faahko manually as shown. It might be best to use a different name in the tutorial.